RetrogeneDB ID: retro_ggor_2615

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:107680132..107681087(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSGGOG00000001579
• Aliases: None
• Description: None

Sequence

>retro_ggor_2615
ATGAAGCTGGTCCTACTGTAGGGCCATGAGCAGGTCATTAGGCAGGTGAAGTATAACTGTGAAGGAGACCTCCTCTTCAC
CGTGGCCAAGGAACCTATCATTAATGCATGATACCCTGTGAATGGTGAGAGGCTGGGCATCTACATGGGCCATACCAGAG
CTGTGTGGTATGTGAACGCTGACTGGGACACCAAGCATGTCCTCACCCATTCAACTGACAACCATCTTTGGGCCTGTGAA
ACAGGGAAACAGCTGGCCCTACTCAAGACCAATTCAACTGTGTGGATCTGCAGTTTTGACTTTGGGGGCAATATCATCAC
GTTCTCCATGGAGAAGCATAAAAGCTATCAGTGCTTTGTGAGCTTCTTTGACCTGCAGGATCTGAGCCAGATTGACAGCA
ATGAGTGCTACCTGAAGATCCCTTGCAATGACTCTAAAATCACTAGTGCCATTTGGGGCTCCTGTGGGGAGTGCATCATT
GCAGGCCATGAGAGTGGAAAGCTCAACCAGTATAGTGCCAAGCCTGGAGAGGTGTTGGTGAATATTAAGGAGCACTCCTA
GCAGATTAATGACATCCAGTTATCCAGGGACATGATCGTCTTTGTCACTGCATCCAAAGACAGCACAGCCAAGCTTTTTG
ACTCTACAACTCTTCAACATCAGAAGACTTTCTGAACAGAAAGCCCCATCAGCTCAGCTACCCTCTCCCCCAACTGTGAC
CATATTGTGCTGGGCGGTGGTCAGGAAGCCATGGATGTAACCACAACCTTCACTAGGATTGGCAAGTTTGAGTCCGGGTT
CCTCCATTTGGCCTTTGAAGAAGAGTTCAGAAGAGTCAAGGGGCACTTTGGACCTATCAACAGTGTTGCCTTCCATCCTG
ATGGCAAGAGCTACAGCAGTGGCAGTGAGGATGGTTACATCCATAATCTACTACTTTAATACACAGTACTTTGAA

Alignment

ORF - retro_ggor_2615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 98.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDADWDTKHVLTG
          MK..LL.GHE..I.Q.KYN.EGDLLFTVAK.PI.N..Y.VNGERLG.YMGHT.AVW.V.ADWDTKHVLT.
Retrocopy MKLVLL*GHEQVIRQVKYNCEGDLLFTVAKEPIINA*YPVNGERLGIYMGHTRAVWYVNADWDTKHVLTH

Parental  SADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYM
          S.DN...LW.CETGKQLALLKTNS.V..C.FDFGGNII.FS..K...YQCFVSFFDL.D.SQID.NE.Y.
Retrocopy STDN--HLWACETGKQLALLKTNSTVWICSFDFGGNIITFSMEKHKSYQCFVSFFDLQDLSQIDSNECYL

Parental  KIPCNDSKITSAVWGPLGECIIAGHESGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDN
          KIPCNDSKITSA.WG..GECIIAGHESG.LNQYSAK.GEVLVN.KEHS.QINDIQLSRDM..FVTASKD.
Retrocopy KIPCNDSKITSAIWGSCGECIIAGHESGKLNQYSAKPGEVLVNIKEHS*QINDIQLSRDMIVFVTASKDS

Parental  TAKLFDSTTLEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGR
          TAKLFDSTTL.HQKTF.TE.P..SA.LSPN.DH.VLGGGQEAMDVTTT.TRIGKFE..F.HLAFEEEF.R
Retrocopy TAKLFDSTTLQHQKTF*TESPISSATLSPNCDHIVLGGGQEAMDVTTTFTRIGKFESGFLHLAFEEEFRR

Parental  VKGHFGPINSVAFHPDGKSYSSGGEDGYVR-IHYFDPQYFE
          VKGHFGPINSVAFHPDGKSYSSG.EDGY...I.YF..QYFE
Retrocopy VKGHFGPINSVAFHPDGKSYSSGSEDGYIH>IYYFNTQYFE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	54.28 RPM
SRP007412_cerebellum	0.00 RPM	46.84 RPM
SRP007412_heart	0.00 RPM	31.74 RPM
SRP007412_kidney	0.00 RPM	81.49 RPM
SRP007412_liver	0.00 RPM	41.44 RPM
SRP007412_testis	0.00 RPM	75.32 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2615 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3888
Pongo abelii	retro_pabe_3169

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615 , retro_ggor_2623,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,